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- PDB-4mkp: Crystal structure of human cGAS apo form -

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Basic information

Entry
Database: PDB / ID: 4mkp
TitleCrystal structure of human cGAS apo form
ComponentsCyclic GMP-AMP synthase
KeywordsTRANSFERASE / nucleotidyltransferase
Function / homology
Function and homology information


cyclic GMP-AMP synthase / 2',3'-cyclic GMP-AMP synthase activity / STING mediated induction of host immune responses / paracrine signaling / poly-ADP-D-ribose modification-dependent protein binding / regulation of immunoglobulin production / cGAS/STING signaling pathway / pattern recognition receptor signaling pathway / regulation of T cell activation / cytoplasmic pattern recognition receptor signaling pathway ...cyclic GMP-AMP synthase / 2',3'-cyclic GMP-AMP synthase activity / STING mediated induction of host immune responses / paracrine signaling / poly-ADP-D-ribose modification-dependent protein binding / regulation of immunoglobulin production / cGAS/STING signaling pathway / pattern recognition receptor signaling pathway / regulation of T cell activation / cytoplasmic pattern recognition receptor signaling pathway / negative regulation of cGAS/STING signaling pathway / cGMP-mediated signaling / cellular response to exogenous dsRNA / positive regulation of type I interferon production / negative regulation of double-strand break repair via homologous recombination / nucleosome binding / positive regulation of defense response to virus by host / phosphatidylinositol-4,5-bisphosphate binding / activation of innate immune response / cAMP-mediated signaling / molecular condensate scaffold activity / determination of adult lifespan / positive regulation of cellular senescence / site of double-strand break / double-stranded DNA binding / defense response to virus / nuclear body / DNA repair / innate immune response / DNA damage response / chromatin binding / GTP binding / protein homodimerization activity / DNA binding / nucleoplasm / ATP binding / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Beta Polymerase; domain 2 - #90 / Poly(a)-polymerase, middle domain - #40 / Poly(a)-polymerase, middle domain / Mab-21-like, nucleotidyltransferase domain / Mab-21-like, HhH/H2TH-like domain / Mab-21 protein HhH/H2TH-like domain / Mab-21 protein nucleotidyltransferase domain / Mab-21-like / Mab-21 / Beta Polymerase; domain 2 ...Beta Polymerase; domain 2 - #90 / Poly(a)-polymerase, middle domain - #40 / Poly(a)-polymerase, middle domain / Mab-21-like, nucleotidyltransferase domain / Mab-21-like, HhH/H2TH-like domain / Mab-21 protein HhH/H2TH-like domain / Mab-21 protein nucleotidyltransferase domain / Mab-21-like / Mab-21 / Beta Polymerase; domain 2 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Cyclic GMP-AMP synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.953 Å
AuthorsKato, K. / Ishii, R. / Ishitani, R. / Nureki, O.
CitationJournal: Plos One / Year: 2013
Title: Structural and Functional Analyses of DNA-Sensing and Immune Activation by Human cGAS
Authors: Kato, K. / Ishii, R. / Goto, E. / Ishitani, R. / Tokunaga, F. / Nureki, O.
History
DepositionSep 5, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cyclic GMP-AMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6142
Polymers42,5491
Non-polymers651
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)123.546, 48.311, 59.565
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1164-

HOH

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Components

#1: Protein Cyclic GMP-AMP synthase / cGAMP synthase / cGAS / h-cGAS / Mab-21 domain-containing protein 1


Mass: 42549.039 Da / Num. of mol.: 1 / Fragment: UNP residues 161-522
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MB21D1 / Plasmid: modified pE-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8N884, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: PEG 3350, NH4NO3, NaCl, CYMAL-7, pH 7.5, vapor diffusion, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorDate: May 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 26029 / Biso Wilson estimate: 32.26 Å2

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.2_869refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K96

4k96


Resolution: 1.953→42.878 Å / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8311 / SU ML: 0.39 / σ(F): 1.35 / Phase error: 23.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2523 1311 5.04 %
Rwork0.2045 --
obs0.2069 25996 97.59 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.919 Å2 / ksol: 0.363 e/Å3
Displacement parametersBiso max: 117.23 Å2 / Biso mean: 50.7263 Å2 / Biso min: 15.51 Å2
Baniso -1Baniso -2Baniso -3
1--0.6049 Å2-0 Å20 Å2
2---5.3965 Å20 Å2
3---6.0015 Å2
Refinement stepCycle: LAST / Resolution: 1.953→42.878 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2526 0 1 114 2641
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112605
X-RAY DIFFRACTIONf_angle_d1.2463519
X-RAY DIFFRACTIONf_chiral_restr0.086400
X-RAY DIFFRACTIONf_plane_restr0.004441
X-RAY DIFFRACTIONf_dihedral_angle_d17.134953
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9531-2.03130.2951230.24422616273995
2.0313-2.12370.25911360.21862691282797
2.1237-2.23570.26311380.20522689282797
2.2357-2.37570.24841540.18952705285998
2.3757-2.55910.26041730.19612680285397
2.5591-2.81660.25171320.20352753288598
2.8166-3.22410.26961510.20552775292698
3.2241-4.06150.24351600.19132808296899
4.0615-42.88850.24271440.2122968311299
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.9036-0.32180.36512.72572.43418.82260.17770.32410.3742-0.4341-0.15210.0981-0.7472-0.3951-0.1140.46970.0170.06350.30450.01940.33466.499726.259316.2489
23.7394-0.32260.28283.469-0.66673.8940.01880.3863-0.209-0.6189-0.061-0.0991-0.1450.16210.15760.41480.10280.08190.467-0.04440.22316.51769.62150.2165
32.4736-0.0178-0.46212.166-0.36492.5340.16670.50950.0825-0.5885-0.0824-0.3235-0.09650.344-0.01810.3290.03330.07840.3509-0.01220.241814.75268.96567.2602
42.66310.5683-0.37832.69310.38071.98170.1314-0.36280.08850.1267-0.0687-0.4642-0.140.5811-0.05560.1453-0.0234-0.04350.25870.00720.201319.298813.90127.692
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 162:197)A162 - 197
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 198:272)A198 - 272
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 273:388)A273 - 388
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 389:521)A389 - 521

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